This study interprets the recent history of Lake Kivu, a tropical lake in the East African Rift Valley. The current gross sedimentation was characterized from a moored sediment trap array deployed over 2 years. The past net sedimentation was investigated with three short cores from two different basins. Diatom assemblages from cores were interpreted as reflecting changes in mixing depth, surface salinity and nutrient availability. The contemporary sediment trap data indicate seasonal variability, governed by diatom blooms during the annual mixing in the dry season, similar to Lakes Malawi and Tanganyika. The ratio of settling fluxes to net sediment accumulation rates implies mineralization rates of 80–90% at the sediment-water interface. The sediment cores revealed an abrupt change ~40 years ago, when carbonate precipitation started. Since the 1960s, deep-water methane concentrations, nutrient fluxes and soil mineral inputs have increased considerably and diatom assemblages have altered. These modifications probably resulted from a combination of three factors, commonly altering lake systems: the introduction of a non-native fish species, eutrophication, and hydrological changes inducing greater upwelling. Both the fish introduction and increased rainfall occurred at the time when the onset of carbonate precipitation was observed, whereas catchment population growth accompanied by intensified land use increased the flux of soil minerals already since the early twentieth century due to more intense erosion.